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In N, the player controls a ninja who navigates tile-based levels while simultaneously avoiding hazards, collecting gold, and eventually opening an exit door which completes the level. Gameplay involves four keys — a move-left key (default left arrow), a move-right key (default right arrow), jumping (default shift key), and suicide (default k key). Combination of these moves on various types of terrain allows the ninja to perform a variety of movements, such as jumping from wall to wall, climbing up vertical inclines, and sliding down steep surfaces.

As of version 2.0, N contains one hundred episodes (numbered 00 – 99). Each episode features five levels (numbered 0 – 4). N has a total of 500 maps, 450 of which are made by Metanet Software. The remaining 50 levels are user levels hand-picked by Metanet. The goal of each level is to trigger the switch and exit through the door it opens within the time limit. Some levels have more than one exit and associated switch, giving the player more freedom to decide his route and method of completing the map.

Each episode is given a cumulative time limit. At the beginning of level 0, the player is given 90 seconds to complete the next five levels. The episode's time limit can be increased by collecting gold, which adds two seconds per piece. The time left at the end of each level carries over to the next level. The only exception is the final level, in which the time left becomes that episode's score.

N also contains a feature that adds support for custom, user-made levels. This is done through a built-in level editor called NEd, or the "N Editor". For version 1.4 and 2.0, Metanet selected a handful of fan-made maps that are given to players with the game's download. Levels can be added into a game by modifying a text file accompanying the game that contains user level data. The most significant difference about user levels is that they do not support N's episode structure.

Doors can allow or impede progress throughout levels. With the exception of the exit door, all doors will impede enemies if closed (with exception of the thwump and the floorguard)

Standard doors allow the ninja to move through them freely, and do not impede his progress, while stopping most hazards from passing through (the exception being floorchasers and thwumps).

Locked doors will remain closed and impassable until triggered by a switch, and remain open permanently afterwards.

Trap doors are activated by small gray switches and close. They are often used to trap a player in a chamber or to create a platform for him to jump or run onto. They can also be used to change the direction of drones in the level.

The exit door is opened by a large blue and gray switch, and must be reached to complete a level.

Gauss Turrets aim at the ninja using an advanced algorithm based on the ninja's distance and movement relative to the turret. They continue to aim so long as the ninja is in their line of sight. Once aimed, they pause for a short moment before firing.

Rocket Turrets launch homing rockets that track the ninja until they collide and detonate upon him, a door, or a tile. Each turret can fire only one rocket at a time.

Stationary Mines are one of the most common hazards in the game. They explode upon coming in contact with the ninja.

Thwumps are square blocks that move in a straight line when the ninja is in sight or a square to the side of it. Only one side of the thwump is lethal, and this side is colored electric blue; the ninja can hold onto, stand, and walk on the other three sides safely. Once a thwump has moved outwards to its maximum extent, it will return slowly. If trapped between a wall and the returning side of a thwump, the ninja will be crushed. In some levels the player must use the thwumps to their advantage.

Zap drones usually follow a simple, pre-set movement pattern. However, there are also "chasing" Seeker Drones, which have an antenna, and rush in a straight line at the ninja if he moves into or perpendicular to their line of sight. The most common enemy besides mines.

Laser Drones move slowly and fire a red laser beam at the ninja's location. They take a short time to power up, and their laser, a straight line between the drone and the ninja's location, stays active for a short time (approx. 3 seconds) afterward.

Chaingun drones fire a stream of inaccurate bullets at the ninja; these also take a few seconds to power up.

Floorchasers/Floorguards rush at the ninja if he is on the same level that the floorchaser is on. They accelerate instantly and move slightly faster than the ninja running at full speed.

The ninja can also die by hitting the environment at excess speed; this scenario however, is valid only in the case where the ninja hits a surface perpendicular to the direction of jump/fall. The most common example is falling straight down to a flat surface from a certain height, but can also include more unusual situations like falling diagonally toward an incline or wall-jumping too aggressively and thereby flying into the ceiling at a dangerous speed. Landing on a spike is possible, but can kill the ninja if he jumps on it from a lower height than a perpendicular tile.

Launchpads are used to propel the ninja in various directions at rapid speeds.

Bounce blocks are square blocks that have a "springy" movement when the ninja interacts with them, which can also be used as trampolines. Some may have mines inside them.

One-Way platforms let the ninja move through it in one direction, but not the opposite (with the exception of sliding from curved or sloped surfaces, where you can pass through it the wrong way with ease. You can also launch through it if you get stuck between it and a thwump). The platform is usually used to provide places to stand or limit the ninja's movement.

As of v1.4, the player is rewarded with the ability to change the color of the ninja, or the ninja's flavor. The default flavor is black, and a new color is rewarded after reaching the last level in a column.[3] The flavors are rewarded in a specific order, regardless of which column is completed, and are as follows:

Overclocking is a feature which allows a player to change the speed the game runs at, including the ninja's speed, enemy speed, and the rate that time runs out. This speed setting can range from 0 to 10, with 0 being the normal speed.

Numerous websites, including AddictingGames[4] and eBaum's World,[5] host various versions of N that can be played from inside the browser (in SWF format), often known as "N-Game". These versions of the game violate the game's license agreement, often do not give credit to the original developers, and are out-of-date compared to the latest official version of N. Furthermore, the official N comes packaged with several files that are not included on these websites: as well as the game itself, readmes for the game, cheats and level editor are included, a license text file, as well as a text file for adding in user-made levels.

Metanet Software stated on "the Way of the Ninja" (Official N website) that a new N 2.1 is coming soon, promising better NED (level editor), more levels and even more secrets in the game. Metanet Software also stated that the source code of N will be released with the 2.1 version.[6] Five years after N 1.4 release, on 1 June 2010, Metanet Software announced on the Forums and on the Metablog, that they were going to definitely start with N 1.5. They created some threads in the forums that discussed every new aspect of the new version of N, asking for the players feedback, and asking the players their opinions. In December 2011, a demo of the N v2.0 beta was released in the form of a 'contesque'. Players who ranked highly in each section were awarded with prize packs, including T-shirts, N++ download codes, stickers, buttons and more. On 1 January 2013, version 2.0 was released as a full beta, complete with a new physics engine written in ActionScript 3.0. The official release added a plethora of new episodes and bonus content and minor bug fixes. As of 31 December 2014, 2.0 is the most recent version for PC.